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author | Thomas White <taw@physics.org> | 2010-04-01 18:07:00 +0200 |
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committer | Thomas White <taw@physics.org> | 2010-04-01 18:07:00 +0200 |
commit | efbab41e65b5ca0c19b05eee40eb4a4ebadfd262 (patch) | |
tree | 81e3bb90620480be56cae675162eab886c696efd | |
parent | f318994ea3f7d801a5feccdf253664ca2ff241d7 (diff) |
indexamajig: Improve --help
-rw-r--r-- | src/indexamajig.c | 28 |
1 files changed, 17 insertions, 11 deletions
diff --git a/src/indexamajig.c b/src/indexamajig.c index 46109a76..48833db2 100644 --- a/src/indexamajig.c +++ b/src/indexamajig.c @@ -82,17 +82,19 @@ static void show_help(const char *s) " --indexing=<method> Use 'method' for indexing. Choose from:\n" " none : no indexing\n" " dirax : invoke DirAx\n" -"\n" -" --verbose Be verbose about indexing.\n" -" --gpu Use the GPU to speed up the simulation.\n" -" -j <n> Run <n> analyses in parallel. Default 1.\n" -"\n" +"\n\nWith just the above options, this program does not do much of practical " +"use.\nYou should also enable some of the following:\n\n" " --near-bragg Output a list of reflection intensities to stdout.\n" -" The intensities in this list are the sum of\n" -" the values in a 7x7 square centered on the pixel\n" -" closest to the Bragg condition. Only pixels with\n" -" fractional indices within 0.1 of the Bragg\n" -" condition will be counted.\n" +" When pixels with fractional indices within 0.1 of\n" +" integer values (the Bragg condition) are found,\n" +" the integral of pixels within a ten pixel radius\n" +" of the nearest-to-Bragg pixel will be reported as\n" +" the intensity. The centroid of the pixels will\n" +" be given as the coordinates, as well as the h,k,l\n" +" (integer) indices of the reflection. If a peak\n" +" was located by the initial peak search close to\n" +" the \"near Bragg\" location, its coordinates will\n" +" be taken as the centre instead.\n" " --simulate Simulate the diffraction pattern using the indexed\n" " unit cell.\n" " --filter-cm Perform common-mode noise subtraction on images\n" @@ -102,7 +104,6 @@ static void show_help(const char *s) " pixels in each 3x3 region to zero if any of them\n" " have negative values. Intensity measurement will\n" " be performed on the image as it was before this.\n" -"\n" " --write-drx Write 'xfel.drx' for visualisation of reciprocal\n" " space. Implied by any indexing method other than\n" " 'none'. Beware: the units in this file are\n" @@ -113,6 +114,11 @@ static void show_help(const char *s) " --no-match Don't attempt to match the indexed cell to the\n" " model, just proceed with the one generated by the\n" " auto-indexing procedure.\n" +"\n\nOptions for greater performance or verbosity:\n\n" +" --verbose Be verbose about indexing.\n" +" --gpu Use the GPU to speed up the simulation.\n" +" -j <n> Run <n> analyses in parallel. Default 1.\n" +"\n\nControl of model and data input:\n\n" " --intensities=<file> Specify file containing reflection intensities\n" " to use when simulating.\n" " -p, --pdb=<file> PDB file from which to get the unit cell to match.\n" |